Zinc in PDB 1d5j: Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.

All present enzymatic activity of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.:
3.4.24.17;

The structure of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor., PDB code: 1d5j was solved by N.G.Almstead, R.S.Bradley, S.Pikul, B.De, M.G.Natchus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.780, 78.540, 105.270, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 25.7

The structure of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. (pdb code 1d5j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor., PDB code: 1d5j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.0 occ:1.00 OB A:MM3401 1.8 20.0 1.0 OA A:MM3401 1.9 2.0 1.0 NE2 A:HIS201 2.1 6.3 1.0 NE2 A:HIS211 2.3 2.8 1.0 NE2 A:HIS205 2.4 5.1 1.0 C A:MM3401 2.6 15.5 1.0 NA A:MM3401 2.8 9.5 1.0 CD2 A:HIS201 3.1 5.5 1.0 CE1 A:HIS201 3.2 6.0 1.0 CD2 A:HIS211 3.2 3.2 1.0 CD2 A:HIS205 3.3 9.3 1.0 CE1 A:HIS211 3.3 2.0 1.0 CE1 A:HIS205 3.5 2.0 1.0 OE2 A:GLU202 3.7 7.6 1.0 C13 A:MM3401 4.0 16.7 1.0 CG A:HIS201 4.3 3.6 1.0 ND1 A:HIS201 4.3 3.6 1.0 ND1 A:HIS211 4.4 2.0 1.0 CG A:HIS211 4.4 4.2 1.0 CG A:HIS205 4.5 7.1 1.0 ND1 A:HIS205 4.5 2.0 1.0 C6 A:MM3401 4.6 2.0 1.0 CD A:GLU202 4.6 2.0 1.0 C5 A:MM3401 4.8 3.9 1.0 OE1 A:GLU202 4.8 10.1 1.0 CE A:MET219 4.9 2.0 1.0 C14 A:MM3401 4.9 15.5 1.0 N12 A:MM3401 4.9 14.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.8 occ:1.00 ND1 A:HIS179 2.0 4.3 1.0 NE2 A:HIS151 2.0 2.9 1.0 NE2 A:HIS166 2.1 13.0 1.0 OD2 A:ASP153 2.1 9.4 1.0 CE1 A:HIS179 2.9 2.8 1.0 CE1 A:HIS151 3.0 6.5 1.0 CD2 A:HIS166 3.0 12.9 1.0 CD2 A:HIS151 3.1 5.5 1.0 CG A:ASP153 3.1 16.6 1.0 CG A:HIS179 3.1 4.4 1.0 CE1 A:HIS166 3.1 13.5 1.0 OD1 A:ASP153 3.3 23.9 1.0 CB A:HIS179 3.6 4.8 1.0 NE2 A:HIS179 4.0 2.0 1.0 OH A:TYR168 4.1 6.6 1.0 ND1 A:HIS151 4.1 2.0 1.0 CG A:HIS151 4.2 4.2 1.0 CD2 A:HIS179 4.2 2.0 1.0 CG A:HIS166 4.2 9.1 1.0 ND1 A:HIS166 4.3 9.7 1.0 O A:TYR155 4.3 14.9 1.0 CB A:ASP153 4.4 15.0 1.0 CZ A:PHE157 4.6 2.6 1.0 CE1 A:TYR168 4.7 3.9 1.0 CZ A:TYR168 4.9 2.5 1.0 O A:HOH403 4.9 9.3 1.0 CE1 A:PHE157 5.0 3.0 1.0 CE2 A:PHE157 5.0 3.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:34.6 occ:1.00 OB B:MM3901 1.9 29.0 1.0 OA B:MM3901 1.9 20.6 1.0 NE2 B:HIS701 2.2 8.6 1.0 NE2 B:HIS711 2.2 20.4 1.0 NE2 B:HIS705 2.2 10.7 1.0 C B:MM3901 2.5 24.3 1.0 NA B:MM3901 2.6 21.3 1.0 CD2 B:HIS705 3.0 11.7 1.0 CE1 B:HIS701 3.1 9.3 1.0 CD2 B:HIS711 3.1 19.6 1.0 CE1 B:HIS711 3.2 18.7 1.0 CD2 B:HIS701 3.2 11.7 1.0 CE1 B:HIS705 3.3 11.1 1.0 C13 B:MM3901 3.9 24.0 1.0 CG B:HIS705 4.2 9.0 1.0 OE2 B:GLU702 4.3 12.7 1.0 ND1 B:HIS705 4.3 5.8 1.0 ND1 B:HIS711 4.3 22.3 1.0 ND1 B:HIS701 4.3 9.3 1.0 CG B:HIS711 4.3 20.5 1.0 CG B:HIS701 4.3 9.9 1.0 C6 B:MM3901 4.4 24.1 1.0 C1 B:MM3901 4.6 19.9 1.0 C14 B:MM3901 4.8 20.4 1.0 C5 B:MM3901 4.9 23.7 1.0 N12 B:MM3901 5.0 22.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:14.7 occ:1.00 OD2 B:ASP653 2.0 14.9 1.0 NE2 B:HIS666 2.0 10.1 1.0 ND1 B:HIS679 2.1 5.6 1.0 NE2 B:HIS651 2.3 11.2 1.0 CE1 B:HIS666 3.0 7.0 1.0 CE1 B:HIS679 3.0 5.0 1.0 CG B:HIS679 3.0 6.7 1.0 CD2 B:HIS651 3.0 9.4 1.0 CG B:ASP653 3.0 13.4 1.0 CD2 B:HIS666 3.1 7.6 1.0 CE1 B:HIS651 3.4 11.6 1.0 CB B:HIS679 3.4 8.5 1.0 OD1 B:ASP653 3.5 18.7 1.0 NE2 B:HIS679 4.0 4.3 1.0 O B:TYR655 4.0 15.0 1.0 CD2 B:HIS679 4.1 7.8 1.0 ND1 B:HIS666 4.1 7.8 1.0 CG B:HIS666 4.2 5.8 1.0 CG B:HIS651 4.3 7.9 1.0 CB B:ASP653 4.3 7.3 1.0 OH B:TYR668 4.4 14.9 1.0 ND1 B:HIS651 4.4 8.2 1.0 CZ B:PHE657 4.6 3.2 1.0 CE1 B:PHE657 4.7 7.4 1.0 CE1 B:TYR668 4.8 12.2 1.0 CA B:HIS679 4.9 7.5 1.0

N.G.Almstead, R.S.Bradley, S.Pikul, B.De, M.G.Natchus, Y.O.Taiwo, F.Gu, L.E.Williams, B.A.Hynd, M.J.Janusz, C.M.Dunaway, G.E.Mieling. Design, Synthesis, and Biological Evaluation of Potent Thiazine- and Thiazepine-Based Matrix Metalloproteinase Inhibitors. J.Med.Chem. V. 42 4547 1999.
ISSN: ISSN 0022-2623
PubMed: 10579818
DOI: 10.1021/JM990330Y